@@ -1,5 +1,8 @@

 CHANGES IN VERSION 1.5.2

 ------------------------

+ o add extend, extendto parameter in geom_hilight <2016-05-10, Tue>

+ o geom_hilight now supports hilight tips <2016-05-10, Tue>

+   + https://github.com/GuangchuangYu/ggtree/issues/53

  o more accurate ylim & angle for circular layout <2016-05-10, Tue>

    + https://github.com/GuangchuangYu/ggtree/issues/40

  o supports phylo4d object <2016-05-10, Tue>

@@ -5,12 +5,14 @@

 ##' @param node selected node to hilight

 ##' @param fill color fill

 ##' @param alpha alpha (transparency)

+##' @param extend extend xmax of the rectangle

+##' @param extendto extend xmax to extendto

 ##' @return ggplot2

 ##' @export

 ##' @importFrom ggplot2 aes_

 ##' @importFrom ggplot2 GeomRect

 ##' @author Guangchuang Yu

-geom_hilight <- function(node, fill="steelblue", alpha=.5) {

+geom_hilight <- function(node, fill="steelblue", alpha=.5, extend=0, extendto=NULL) {

     data = NULL

@@ -33,7 +35,10 @@ geom_hilight <- function(node, fill="steelblue", alpha=.5) {

         show.legend=show.legend,

         inherit.aes = inherit.aes,

         params = list(node=node,

-                      fill=fill, alpha=alpha,

+                      fill=fill,

+                      alpha=alpha,

+                      extend=extend,

+                      extendto=extendto,

                       na.rm = na.rm)

     )

 }

@@ -51,6 +56,8 @@ geom_hilight <- function(node, fill="steelblue", alpha=.5) {

 ##' @param inherit.aes logical

 ##' @param fill fill color

 ##' @param alpha transparency

+##' @param extend extend xmax of the rectangle

+##' @param extendto extend xmax to extendto

 ##' @param ... additional parameter

 ##' @return layer

 ##' @importFrom ggplot2 layer

@@ -58,7 +65,7 @@ geom_hilight <- function(node, fill="steelblue", alpha=.5) {

 stat_hilight <- function(mapping=NULL, data=NULL, geom="rect",

                          position="identity",  node, 

                          show.legend=NA, inherit.aes=FALSE,

-                        fill, alpha,

+                        fill, alpha, extend=0, xmax=NULL,

                          ...) {

     default_aes <- aes_(x=~x, y=~y, node=~node, parent=~parent, branch.length=~branch.length)

     if (is.null(mapping)) {

@@ -76,8 +83,9 @@ stat_hilight <- function(mapping=NULL, data=NULL, geom="rect",

         show.legend=show.legend,

         inherit.aes = inherit.aes,

         params = list(node=node,

-            fill=fill, alpha=alpha,

-            ...)

+                      fill=fill, alpha=alpha,

+                      extend=extend, extendto=extendto,

+                      ...)

         )

 }

@@ -88,8 +96,17 @@ stat_hilight <- function(mapping=NULL, data=NULL, geom="rect",

 ##' @importFrom ggplot2 Stat

 ##' @export

 StatHilight <- ggproto("StatHilight", Stat,

-                       compute_group = function(self, data, scales, params, node) {

-                           get_clade_position_(data, node)

+                       compute_group = function(self, data, scales, params, node, extend, extendto) {

+                           df <- get_clade_position_(data, node)

+                           df$xmax <- df$xmax + extend

+                           if (!is.null(extendto) && !is.na(extendto)) {

+                               if (extendto < df$xmax) {

+                                   warning("extendto is too small, keep the original xmax value...")

+                               } else {

+                                   df$xmax <- extendto

+                               }

+                           }

+                           return(df)

                        },

                        required_aes = c("x", "y", "branch.length")

                        )

@@ -109,14 +126,22 @@ get_clade_position <- function(treeview, node) {

 }

 get_clade_position_ <- function(data, node) {

-    sp <- get.offspring.df(data, node)

-    ## sp.df <- data[c(sp, node),]

-    sp <- c(sp, node)

-    sp.df <- data[match(sp, data$node),]

+    sp <- tryCatch(get.offspring.df(data, node), error=function(e) NULL)

+

+    i <- match(node, data$node)

+    if (is.null(sp)) {

+        ## tip

+        sp.df <- data[i,]

+    } else {

+        sp <- c(sp, node)

+        sp.df <- data[match(sp, data$node),]

+    }

+

     x <- sp.df$x

     y <- sp.df$y

+    

     if ("branch.length" %in% colnames(data)) {

-        xmin <- min(x)-data[match(node, data$node), "branch.length"]/2

+        xmin <- min(x)-data[i, "branch.length"]/2

     } else {

         xmin <- min(sp.df$branch)

     }

@@ -4,7 +4,8 @@

 \alias{geom_hilight}

 \title{geom_hilight}

 \usage{

-geom_hilight(node, fill = "steelblue", alpha = 0.5)

+geom_hilight(node, fill = "steelblue", alpha = 0.5, extend = 0,

+  extendto = NULL)

 }

 \arguments{

 \item{node}{selected node to hilight}

@@ -12,6 +13,10 @@ geom_hilight(node, fill = "steelblue", alpha = 0.5)

 \item{fill}{color fill}

 \item{alpha}{alpha (transparency)}

+

+\item{extend}{extend xmax of the rectangle}

+

+\item{extendto}{extend xmax to extendto}

 }

 \value{

 ggplot2

@@ -6,7 +6,7 @@

 \usage{

 stat_hilight(mapping = NULL, data = NULL, geom = "rect",

   position = "identity", node, show.legend = NA, inherit.aes = FALSE,

-  fill, alpha, ...)

+  fill, alpha, extend = 0, xmax = NULL, ...)

 }

 \arguments{

 \item{mapping}{aes mapping}

@@ -27,7 +27,11 @@ stat_hilight(mapping = NULL, data = NULL, geom = "rect",

 \item{alpha}{transparency}

+\item{extend}{extend xmax of the rectangle}

+

 \item{...}{additional parameter}

+

+\item{extendto}{extend xmax to extendto}

 }

 \value{

 layer